Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents

Allioux, Maxime; Yvenou, Stéven; Slobodkina, G. B.; Slobodkin, A. I.; Shao, Zongze; Jebbar, Mohamed; Alain, Karine

doi:10.3390/microorganisms8081132

Cited by 14 publications

(15 citation statements)

References 39 publications

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“…Occurrence localities to build the models were taken from the GBIF database (accessed on October 2019) [56][57][58] and were subsequently filtered to eliminate dubious occurrences and all continental data. This database has been widely used for ecological studies of macro and microorganisms throughout the globe [59][60][61]. Duplicated occurrences (with the same coordinates) were also eliminated to ensure independence among occurrences.…”

Section: Niche Modelmentioning

confidence: 99%

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

Tenelanda-Osorio

Parra

Cuartas-Restrepo

et al. 2021

Life

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Enceladus is a potential target for future astrobiological missions. NASA’s Cassini spacecraft demonstrated that the Saturnian moon harbors a salty ocean beneath its icy crust and the existence and analysis of the plume suggest water–rock reactions, consistent with the possible presence of hydrothermal vents. Particularly, the plume analysis revealed the presence of molecular hydrogen, which may be used as an energy source by microorganisms ( e.g., methanogens). This could support the possibility that populations of methanogens could establish in such environments if they exist on Enceladus. We took a macroscale approximation using ecological niche modeling to evaluate whether conditions suitable for methanogenic archaea on Earth are expected in Enceladus. In addition, we employed a new approach for computing the biomass using the Monod growth model. The response curves for the environmental variables performed well statistically, indicating that simple correlative models may be used to approximate large-scale distributions of these genera on Earth. We found that the potential hydrothermal conditions on Enceladus fit within the macroscale conditions identified as suitable for methanogens on Earth, and estimated a concentration of 1010–1011 cells/cm3.

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Section: Niche Modelmentioning

confidence: 99%

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

Tenelanda-Osorio

Parra

Cuartas-Restrepo

et al. 2021

Life

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“…The selection was based in one of two criteria. Firstly, a genome was reported in the literature to possess the DsrAB proteins [14,18,45,[56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72]. The presence of DsrAB proteins was validated using the rBBHs of DsrAB proteins following same rBBH strategy as in the complete genome dataset.…”

Section: Methods Validation and Comparisonmentioning

confidence: 99%

“…A second dataset (from now on referred to as the metagenomic dataset) composed of the protein sequences of 193 978 prokaryotic (meta)genomic assemblies and 1900 (meta) genomes belonging to potential new lineages with the ability to use the Dsr-dependent dissimilatory sulphur metabolism [14,18,45,[56][57][58][59][60][61][62][63][64][65][66][67][68][69][70][71][72] was created (Table S3). These additional 1900 (meta)genomes were collected from a survey of recent publications describing potential micro-organisms containing Dsr proteins in the following manner: all assemblies related to the publication BioProject (described or not in the text as a micro-organism having the Dsr pathway) were downloaded and added to the metagenomic dataset, if not already present.…”

Section: Genomic Datasetsmentioning

confidence: 99%

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

Neukirchen

Sousa

2021

Microbial Genomics

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Current methods in comparative genomic analyses for metabolic potential prediction of proteins involved in, or associated with the Dsr (dissimilatory sulphite reductase)-dependent dissimilatory sulphur metabolism are both time-intensive and computationally challenging, especially when considering metagenomic data. We developed DiSCo, a Dsr-dependent dissimilatory sulphur metabolism classification tool, which automatically identifies and classifies the protein type from sequence data. It takes user-supplied protein sequences and lists the identified proteins and their classification in terms of protein family and predicted type. It can also extract the sequence data from user-input to serve as basis for additional downstream analyses. DiSCo provides the metabolic functional prediction of proteins involved in Dsr-dependent dissimilatory sulphur metabolism with high levels of accuracy in a fast manner. We ran DiSCo against a dataset composed of over 190 thousand (meta)genomic records and efficiently mapped Dsr-dependent dissimilatory sulphur proteins in 1798 lineages across both prokaryotic domains. This allowed the identification of new micro-organisms belonging to Thaumarchaeota and Spirochaetes lineages with the metabolic potential to use the Dsr-pathway for energy conservation. DiSCo is implemented in Perl 5 and freely available under the GNU GPLv3 at https://github.com/Genome-Evolution-and-Ecology-Group-GEEG/DiSCo.

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“…Whole genome sequencing of both strains was performed by the Fasteris company (Planles-Ouates, Swizerland), using the Illumina MiSeq technology (2 × 150 bp paired-reads; MicroV2 chemistry). Quality control, genome assembly and annotation were performed as described by Allioux et al [38]. Briefly, quality controls of reads were performed by the sequencing facilities while genomes were assembled into contigs, using default parameters, by using the Shovill pipeline (v1.0.9) with SKESA and SPAdes genome assemblers for strain HW T2.11 T and strain HW T5.17 T , respectively.…”

Section: Genome Sequencing Assembly and Annotationmentioning

confidence: 99%

Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate

et al. 2021

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Two novel strains, HW T2.11T and HW T5.17T, were isolated from decaying wood (forest of Champenoux, France). Study of the 16S rRNA sequence similarity indicated that the novel strains belong to the genus Acidisoma. The sequence similarity of the 16S rRNA gene of HW T2.11T with the corresponding sequences of A. tundrae and A. sibiricum was 97.30% and 97.25%, while for HW T5.17T it was 96.85% and 97.14%, respectively. The DNA G+C contents of the strains were 62.32–62.50%. Cells were Gram-negative coccobacilli that had intracellular storage granules (poly-3-hydroxybutyrate (P3HB)) that confer resistance to environmental stress conditions. They were mesophilic and acidophilic organisms growing at 8–25 °C, at a pH of 2.0–6.5, and were capable of using a wide range of organic compounds and complex biopolymers such as starch, fucoidan, laminarin, pectin and cellulose, the latter two being involved in wood composition. The major cellular fatty acid was cyclo C19:0ω8c and the major quinone was Q-10. Overall, genome relatedness indices between genomes of strains HW T2.11T and HW T5.17T (Orthologous Average Nucleotide Identity (OrthoANI) value = 83.73% and digital DNA-DNA hybridization score = 27.5%) confirmed that they belonged to two different species. Genetic predictions indicate that the cyclopropane fatty acid (CFA) pathway is present, conferring acid-resistance properties to the cells. The two novel strains might possess a class IV polyhydroxyalcanoate (PHA) synthase operon involved in the P3HB production pathway. Overall, the polyphasic taxonomic analysis shows that these two novel strains are adapted to harsh environments such as decaying wood where the organic matter is difficult to access, and can contribute to the degradation of dead wood. These strains represent novel species of the genus Acidisoma, for which the names Acidisoma silvae sp. nov. and Acidisoma cellulosilytica sp. nov. are proposed. The type strains of Acidisoma silvae and Acidisoma cellulosilytica are, respectively, HW T2.11T (DSM 111006T; UBOCC-M-3364T) and HW T5.17T (DSM 111007T; UBOCC-M-3365T).

show abstract

Genomic Characterization and Environmental Distribution of a Thermophilic Anaerobe Dissulfurirhabdus thermomarina SH388T Involved in Disproportionation of Sulfur Compounds in Shallow Sea Hydrothermal Vents

Cited by 14 publications

References 39 publications

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

Enceladus as a Potential Niche for Methanogens and Estimation of Its Biomass

DiSCo: a sequence-based type-specific predictor of Dsr-dependent dissimilatory sulphur metabolism in microbial data

Acidisoma silvae sp. nov. and Acidisomacellulosilytica sp. nov., Two Acidophilic Bacteria Isolated from Decaying Wood, Hydrolyzing Cellulose and Producing Poly-3-hydroxybutyrate

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